Difference between revisions of "HMM PD00154"
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Latest revision as of 18:49, 14 October 2015
Back to List of HMMs
Symbol: VSP_VSD
Name: VSP, voltage sensor domain
Why built the HMM?
Voltage sensing domain is a transmembrane domain consists of four helix. There is no available profile in public database. The region is annotated as a part of much larger conserved region.
How the HMM is built
We PSI-BLASTed the region 65-230 of NP_954870.2, based upon the region defined in [1] which used 71-221. The hits included not only VSPs but also other ion channels. We then removed redundant sequences (threshold of sequence identity 70%), aligned them by Clustal Omega program, manually adjusted the alignment, built the HMM profile, and validated it by protein phosphatases of the nine genomes.
